[petsc-users] Reading VTK files in PETSc

[Jed Brown]

I assume you're working with a DA, in which case you can write in HDF5 format and add an Xdmf header so Paraview can read it. The utility lib/petsc/bin/petsc_gen_xdmf.py should be able to handle it.

I haven't written support for it (my problems are unstructured so I've focused on DMPlex), but the CGNS format supports structured meshes and that would be an efficient parallel format that doesn't need a header.

"Kevin G. Wang" <kevinw3 at vt.edu> writes:

> Hi Jed,
>
> Thanks for your help! It does not have to be VTK (.vtr in my case). But I
> am trying to have a "seamless" workflow between reading, writing, and
> visualization, without the need of format conversions. I opted for VTK
> simply because it is easy to write, and can be directly visualized (using
> Paraview).
>
> Could you please advise as to what is the best practice in my scenario? My
> meshes are Cartesian, but non-uniform.
>
> Thanks,
> Kevin
>
> On Thu, Nov 30, 2023 at 1:02 AM Jed Brown <jed at jedbrown.org> wrote:
>
>> Is it necessary that it be VTK format or can it be PETSc's binary format
>> or a different mesh format? VTK (be it legacy .vtk or the XML-based .vtu,
>> etc.) is a bad format for parallel reading, no matter how much effort might
>> go into an implementation.
>>
>> "Kevin G. Wang" <kevinw3 at vt.edu> writes:
>>
>> > Good morning everyone.
>> >
>> > I use the following functions to output parallel vectors --- "globalVec"
>> in
>> > this example --- to VTK files. It works well, and is quite convenient.
>> >
>> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >   PetscViewer viewer;
>> >   PetscViewerVTKOpen(PetscObjectComm((PetscObject)*dm), filename,
>> > FILE_MODE_WRITE, &viewer);
>> >   VecView(globalVec, viewer);
>> >   PetscViewerDestroy(&viewer);
>> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >
>> > Now, I am trying to do the opposite. I would like to read the VTK files
>> > generated by PETSc back into memory, and assign each one to a Vec. Could
>> > someone let me know how this can be done?
>> >
>> > Thanks!
>> > Kevin
>> >
>> >
>> > --
>> > Kevin G. Wang, Ph.D.
>> > Associate Professor
>> > Kevin T. Crofton Department of Aerospace and Ocean Engineering
>> > Virginia Tech
>> > 1600 Innovation Dr., VTSS Rm 224H, Blacksburg, VA 24061
>> > Office: (540) 231-7547  |  Mobile: (650) 862-2663
>> > URL: https://www.aoe.vt.edu/people/faculty/wang.html
>> > Codes: https://github.com/kevinwgy
>>
>
>
> -- 
> Kevin G. Wang, Ph.D.
> Associate Professor
> Kevin T. Crofton Department of Aerospace and Ocean Engineering
> Virginia Tech
> 1600 Innovation Dr., VTSS Rm 224H, Blacksburg, VA 24061
> Office: (540) 231-7547  |  Mobile: (650) 862-2663
> URL: https://www.aoe.vt.edu/people/faculty/wang.html
> Codes: https://github.com/kevinwgy